We decided to visit the lesser-known island of Amami Ōshima, of the Ryukyū archipelago, because we thought the bigger Okinawa was too touristy and overdeveloped. Amami looked like it was more untouched, and that's exactly what we found. We flew from Fukuoka with a convenient 2-hour flight but there are also two ferry lines that leave Kagoshima at night and arrive there in the morning.
We booked the lovely Halemakana guesthouse owned by a wonderful Japanese surfer couple from Tokyo and among the very few that are available for visitors. Without a car it's impossible to get around (there are a couple of bus lines but they're expensive and unreliable) so we managed to rent one just outside of the airport. The area where we were staying (Tatsugochō), in the north and more beautiful part of the island, where the airport also is, doesn't really have a village, just a few houses along the beach: including a burger shack, a hotel called Busayamamura with a restaurant attached, and one convenience store, where we quickly became loyal customers (because our guesthouse didn't have a kitchen). From there we could drive 20 minutes north to our favorite, secluded beach of Sakibaru (find this on your google maps), but the whole area has many wonderful spots and very little people. Tomori beach, just 5 minutes from the airport is also beautiful and one of the most famous spots for snorkeling; from there you can drive to Cape Ayamaru, a very scenic viewpoint with a cute cafe. On the other northern side of the small peninsula near our guesthouse, there is another nice area with small private beaches, where the probably most expensive resort of the island, Nest, is, with a fancy little restaurant. We instead truly enjoyed the local feel of where we were staying, where we also had the chance to participate in a local folklore dance party at the Busayanamara restaurant we ate the first night. Driving south to the capital of the island Naze could take more than an hour, because roads are small and busy with trucks... but when you pass it you finally arrive at the famous park and beach of Ohama, where you can also visit a small Ocean Exhibition hall and see many sea turtles. From there we drove south to the remote villages near the inland waterfalls of Materyia, and we stopped in Kuninao to have lunch in a adorable little izakaya called Bee lunch run by another surfer couple, where we also met two chatty Japanese men who serenaded us with "O' Sole mio"! On our last night we ate at another very good izakaya in the town of Tsatugo.
One thing to keep in mind when you go to these sub-tropical islands is that typhoons may ruin your plans, like it did for us: we only had one day of sun out of the four we were in Amami, so check the weather patterns of the period you want to go in... Overall you can still enjoy the primordial nature of these places, but be careful of the very dangerous habu snake, which is particularly venomous and found all over Amami.